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Seeds are important microbial vectors, and seed-associated pathogens can be introduced into a country through trade, resulting in yield and quality losses in agriculture. The aim of this study was to characterize the microbial communities associated with barley seeds, and based on which, to develop technical approaches to trace their geographical origins, and to inspect and identify quarantine pathogens. Our analysis defined the core microbiota of barley seed and revealed significant differences in the barley seed-associated microbial communities among different continents, suggesting a strong geographic specificity of the barley seed microbiota. By implementing a machine learning model, we achieved over 95% accuracy in tracing the origin of barley seeds. Furthermore, the analysis of co-occurrence and exclusion patterns provided important insights into the identification of candidate biocontrol agents or microbial inoculants that could be useful in improving barley yield and quality. A core pathogen database was developed, and a procedure for inspecting potential quarantine species associated with barley seed was established. These approaches proved effective in detecting four fungal and three bacterial quarantine species for the first time in the port of China. This study not only characterized the core microbiota of barley seeds but also provided practical approaches for tracing the regional origin of barley and identifying potential quarantine pathogens.
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Bacterias , Hongos , Hordeum , Microbiota , Enfermedades de las Plantas , Semillas , Hordeum/microbiología , Semillas/microbiología , Bacterias/aislamiento & purificación , Bacterias/clasificación , Bacterias/genética , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/prevención & control , Hongos/aislamiento & purificación , Hongos/clasificación , Hongos/genética , China , CuarentenaRESUMEN
The quality and sensory attributes of juices are influenced by their natural microbiota and the microorganisms found on filtration membranes. This study aimed to assess the influence of natural microbiota and specific contaminants, including Candida krusei, Rhodotorula mucilaginosa, Debaryomyces prosopidis, Ralstonia insidiosa, and Lactiplantibacillus paraplantarum, isolated from cranberry juice and its associated industrial filtration membranes, on the characteristics of cranberry juice. Their growth kinetics and impacts on total phenols, total anthocyanins, total proanthocyanins, total organic acids, pH, titratable acidity, and volatile compounds were assessed. During the 42 h fermentation period, Candida krusei and Ralstonia insidiosa exhibited significant growth, increasing by 1-log and 3-log, respectively. The natural microbiota led to a 7% and 6% reduction in anthocyanins and proanthocyanidins, while Candida krusei and Rhodotorula mucilaginosa caused losses of 10% and 7% in proanthocyanidins, respectively. Organic acid content remained stable, except for an 8% decrease caused by Ralstonia insidiosa. Volatile compounds underwent significant increases, particularly in green (703%), winey (100%), mushroom (306%), and fusel (2678%) notes. These findings underscore the rapid impact of microorganisms from natural microbiota and filtration membranes on cranberry juice characteristics, highlighting the importance for beverage industries to prioritize customer safety and satisfaction.
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Manipulación de Alimentos , Jugos de Frutas y Vegetales , Microbiota , Proantocianidinas , Vaccinium macrocarpon , Compuestos Orgánicos Volátiles , Vaccinium macrocarpon/química , Vaccinium macrocarpon/microbiología , Jugos de Frutas y Vegetales/microbiología , Jugos de Frutas y Vegetales/análisis , Compuestos Orgánicos Volátiles/análisis , Compuestos Orgánicos Volátiles/metabolismo , Compuestos Orgánicos Volátiles/química , Proantocianidinas/análisis , Odorantes/análisis , Fermentación , Bacterias/clasificación , Bacterias/aislamiento & purificación , Bacterias/crecimiento & desarrollo , Bacterias/metabolismo , Antocianinas/análisis , Candida/crecimiento & desarrollo , Hongos/clasificación , Hongos/metabolismo , Hongos/aislamiento & purificación , Hongos/crecimiento & desarrolloRESUMEN
Sour bamboo shoots are a traditional fermented delicacy that has garnered appreciation both domestically and internationally. This study investigates the intricate dynamics of microbial communities and volatile flavor compounds primarily derived from salted and pickled bamboo shoots during the fermentation process of Phyllostachys purpurea (PP). The dynamics of microorganisms and volatile flavor compounds were thoroughly examined initially using conventional isolation and cultivation methods in conjunction with high-throughput sequencing (HTS), headspace solid-phase microextraction (HS-SPME), and gas chromatography-mass spectrometry (GC-MS). In addition, we analyzed the core microorganisms responsible for modulating the volatile flavor profile. Our findings revealed 60 volatile compounds, 14 of which were the predominant contributors to the aroma of fermented PP. This group primarily comprised alcohols, aldehydes, and olefins. Notably, our investigation identified Lactobacillus and Candida as the dominant microbial genera during the middle and late stages of fermentation. These two genera exert a significant influence on the formation of characteristic aromas. Furthermore, we discovered that acids, sugars, and proteins pivotally influence the succession of microorganisms. Specifically, acids and soluble sugars drove the transition of Lactococcus to Lactobacillus and Pediococcus, whereas soluble proteins facilitated fungal succession from Candida to Kazachstania and Issatchenkia. These insights shed light on the community structure and succession patterns of flavor compounds throughout the PP fermentation process. Ultimately, they provide a foundation for optimizing the fermentation process and ensuring quality control in the production of sour bamboo shoots.
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Bacterias , Fermentación , Microbiota , Brotes de la Planta , Compuestos Orgánicos Volátiles , Compuestos Orgánicos Volátiles/análisis , Compuestos Orgánicos Volátiles/metabolismo , Brotes de la Planta/química , Brotes de la Planta/microbiología , Brotes de la Planta/metabolismo , Bacterias/clasificación , Bacterias/metabolismo , Bacterias/genética , Bacterias/aislamiento & purificación , Cromatografía de Gases y Espectrometría de Masas , Hongos/metabolismo , Hongos/clasificación , Hongos/aislamiento & purificación , Hongos/genética , Aromatizantes/metabolismo , Alimentos Fermentados/microbiología , Alimentos Fermentados/análisis , Odorantes/análisis , Bambusa/microbiología , Bambusa/metabolismo , Bambusa/química , Microextracción en Fase SólidaRESUMEN
The existence of viable human pathogens in bioaerosols which can cause infection or affect human health has been the subject of little research. In this study, data provided by 10 tropospheric aircraft surveys over Japan in 2014 confirm the existence of a vast diversity of microbial species up to 3,000 m height, which can be dispersed above the planetary boundary layer over distances of up to 2,000 km, thanks to strong winds from an area covered with massive cereal croplands in Northeast (NE) Asia. Microbes attached to aerosols reveal the presence of diverse bacterial and fungal taxa, including potential human pathogens, originating from sewage, pesticides, or fertilizers. Over 266 different fungal and 305 bacterial genera appeared in the 10 aircraft transects. Actinobacteria, Bacillota, Proteobacteria, and Bacteroidetes phyla dominated the bacteria composition and, for fungi, Ascomycota prevailed over Basidiomycota. Among the pathogenic species identified, human pathogens include bacteria such as Escherichia coli, Serratia marcescens, Prevotella melaninogenica, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus saprophyticus, Cutibacterium acnes, Clostridium difficile, Clostridium botulinum, Stenotrophomonas maltophilia, Shigella sonnei, Haemophillus parainfluenzae and Acinetobacter baumannii and health-relevant fungi such as Malassezia restricta, Malassezia globosa, Candida parapsilosis and Candida zeylanoides, Sarocladium kiliense, Cladosporium halotolerans, and Cladosporium herbarum. Diversity estimates were similar at heights and surface when entrainment of air from high altitudes occurred. Natural antimicrobial-resistant bacteria (ARB) cultured from air samples were found indicating long-distance spread of ARB and microbial viability. This would represent a novel way to disperse both viable human pathogens and resistance genes among distant geographical regions.
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Aerosoles , Microbiología del Aire , Bacterias , Hongos , Humanos , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Hongos/genética , Hongos/clasificación , Hongos/aislamiento & purificación , Japón , Aeronaves , Monitoreo del Ambiente/métodos , BiodiversidadRESUMEN
Type 2 diabetes mellitus (T2DM) is globally recognized as a significant health concern, with diabetic foot (DF) identified as a severe long-term complication that can lead to tissue death or amputation. The discovery of the impact of mycobiota, a diverse group of multicellular eukaryotes in the gut microbiome, on the onset of endocrine disorders holds great significance. Therefore, this research aimed to examine variations in fungal mycobiome and identify potential biomarkers for T2DM and T2DM-DF. Fecal and blood samples were collected from 33 individuals with T2DM, 32 individuals with T2DM-DF, and 32 healthy individuals without any health conditions (HC). Blood samples were used for laboratory parameters analysis, while total DNA was extracted from fecal samples and sequenced using Illumina 18s rRNA. Bioinformatics tools were employed to analyze fungal abundance and diversity, revealing differentially expressed fungal species and signature fungi that distinguished between T2DM, T2DM-DF, and HC groups. Firstly, significant alterations in some laboratory parameters were observed among the three groups, which also differed between T2DM and T2DM-DF. The diversity of gut fungi in T2DM and T2DM-DF significantly differed from that of the HC group; however, more pronounced changes were observed in T2DM-DF. Additionally, two significantly altered phyla, Ascomycota and Basidiomycota, were identified with higher Ascomycota abundance but lower Basidiomycota abundance in both the T2DM and T2DM-DF compared to the HC group. Furthermore, the top 15 fungi showing significant changes at the species level included a notable decrease in Rhodotorula_mucilaginosa abundance in patients with T2DM compared to HC and a substantial increase in unclassified_g_Candida abundance specifically seen only among patients with T2DM-DF, but not among those diagnosed with T2DM or HC. Thirdly, KEGG was employed to analyze enzyme expression across the three groups, revealing a more pronounced alteration in gut fungal function within T2DM-DF compared to T2DM. Subsequently, to accurately identify signature fungi in each group, a random forest was utilized to rank the top 15 significant fungi. Notably, 11 fungi were identified as potential biomarkers for distinguishing T2DM or T2DM-DF from HC, while eight fungi could discriminate between T2DM and T2DM-DF. Furthermore, receiver operating characteristic curve (ROC) analysis demonstrated enhanced accuracy of predicted outcomes. These findings suggest that changes in fungal mycobiome are closely associated with the progression and complications of T2DM and DF, offering promising prospects for diagnosis and treatment.
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Biomarcadores , Diabetes Mellitus Tipo 2 , Pie Diabético , Disbiosis , Heces , Microbioma Gastrointestinal , Micobioma , Humanos , Diabetes Mellitus Tipo 2/microbiología , Diabetes Mellitus Tipo 2/complicaciones , Persona de Mediana Edad , Femenino , Masculino , Disbiosis/microbiología , Disbiosis/diagnóstico , Pie Diabético/microbiología , Biomarcadores/sangre , Heces/microbiología , Anciano , Adulto , Ascomicetos , Basidiomycota , Estudios de Casos y Controles , Hongos/aislamiento & purificaciónRESUMEN
We isolated the dark septate endophytic (DSE) fungi from roots of typical plant species in the tundra of Changbai Mountains Nature Reserve, including Rhododendron aureum, R. conferentiatum, Vaccinium uliginosum, and Dryas octopetala, and studied their colonization. We further investigated the DSE community composition and species diversity of the four tundra plant species by using morphological characteristics combined with rDNA ITS sequence analysis. The results showed that DSE formed a typical structure of "microsclerotia" in roots of the four plant species. A total of 69 strains of DSE fungi were isolated from the root samples, belonging to 10 genera, and 12 species. They were Phialocephala fortinii, Alternaria alternata, A. tenuissima, Epicocum nigrum, Canariomyces microsporus, Colletotrichum spaethianum, C. camelliae, Leptophoria sp., Cladosporium cladosporioides, Phoma sp., Cadophora sp., and Discosia italica, respectively. The DSE fungal species diversity was rich, and all these fungal species were firstly reported as DSE fungi in the alpine tundra belt of China. Among them, Phialocephala fortinii was the common and dominant species of all tundra plants. The Simpson, Pielou, and Shannon diversity indices of DSE fungi of the four plant species of tundra differed significantly. Our results showed that tundra plants have rich diversity of DSE fungi, and they can form a good symbiotic relationship, which enhance the adaptability of tundra plants to the harsh environment.
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Biodiversidad , Endófitos , Raíces de Plantas , Endófitos/aislamiento & purificación , Endófitos/clasificación , Endófitos/genética , China , Raíces de Plantas/microbiología , Rhododendron/microbiología , Hongos/clasificación , Hongos/aislamiento & purificación , Hongos/genética , Vaccinium/microbiología , Ascomicetos/aislamiento & purificación , Ascomicetos/clasificación , Ascomicetos/genética , Ecosistema , Alternaria/aislamiento & purificación , Alternaria/clasificación , Alternaria/genéticaRESUMEN
Understanding the composition and spatial distribution patterns of microbial communities in plateau peatland soils is crucial for preserving the structural and functional stability of highland wetlands. We collected 50 soil samples from the core conservation area of Zoige peatland along horizontal and vertical distributions to analyze the soil bacterial and fungal diversity by using high-throughput sequencing technology, combined with Mantel tests and multiple regression on matrices (MRM) statistical methods, as well as the spatial distribution characteristics of community structure similarity at a local scale. The results showed that the dominant soil bacterial and fungal groups were Chloroflexi (accounting for 33.2% and 25.1% of the total bacterial community in horizontal and vertical directions, respectively) and Ascomycota (54.7% and 76.4%). The similarity of microbial community structure in both horizontal and vertical directions decreased with increasing spatial distance of the sampling points. The turnover rates of bacterial and fungal communities in the vertical direction were 8.8 and 8.6 times as those in the horizontal direction, respectively. Based on the relative abundance of the communities, we classified microbes into six groups. As the number of rare species in the community increased, the slope of community distance decay decreased. The conditionally rare or abundant taxa (CRAT) category group showed the most similar spatial distribution characteristics to the total microbial community. Mantel analysis indicated that soil organic carbon, total nitrogen, and available phosphorus were key factors driving the distribution of bacterial and fungal communities in the horizontal direction, while soil organic carbon, available carbon, pH, and soil bulk density were the main factors determining the vertical distribution. MRM analysis further showed that both soil physicochemical indicators and spatial distance significantly affected the assembly of microbial communities, where soil factors explained more about the vertical distribution of microbial communities than the horizontal distribution. The impact of soil factors on microbial community distribution was much greater than that of spatial factors through diffusion limitation. In summary, the microbial communities in the plateau peatland soils exhibited more pronounced vertical distribution differences and environmental response characteristics.
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Bacterias , Hongos , Microbiología del Suelo , China , Bacterias/clasificación , Bacterias/aislamiento & purificación , Bacterias/crecimiento & desarrollo , Bacterias/genética , Hongos/clasificación , Hongos/aislamiento & purificación , Hongos/crecimiento & desarrollo , Humedales , Análisis Espacial , Biodiversidad , Altitud , Suelo/química , Microbiota , Chloroflexi/clasificación , Chloroflexi/crecimiento & desarrollo , Chloroflexi/aislamiento & purificación , Ascomicetos/crecimiento & desarrollo , Ascomicetos/aislamiento & purificaciónRESUMEN
The presence of fungi in tracheal wash (TW) of horses was recently linked to mild-moderate equine asthma, indicating a possible causal role; however, increased numbers of fungi may also stem from asthma-related alteration of tracheal mucus clearance or from environmental exposure. Our objective was to elucidate the association between the presence of fungi in TW and asthma status while controlling for relevant confounders. We conducted a retrospective case-control study involving 73 horses, including 34 controls and 39 asthmatic cases. Each asthmatic horse was matched with a control from the same barn to account for the influence of environmental exposure. All horses underwent respiratory clinical scoring, endoscopy, TW, and bronchoalveolar lavage (BAL). The association between asthma status and presence of TW fungi was tested with multivariable logistic regression modelling, accounting for selected management factors, tracheal mucus accumulation, and selected TW and BAL cytological characteristics, including multinucleated giant cells (MGCs) in the TW. Given the variability in MGC definitions in the literature, particularly concerning their morphology and number of nuclei, we constructed two distinct models for each outcome (asthma status or presence of fungi in TW): one considering MGCs as cells with ≥ 3 nuclei, and another using a criterion of ≥ 10 nuclei. Horses with a tracheal mucus score ≥ 2 exhibited 3.6 to 4.3 higher odds of being asthmatic, depending on the MGC definition. None of the other variables examined were associated with either asthma status or TW fungi detection. Notably, the presence of fungal elements in the TW was not associated with equine asthma.
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Asma , Hongos , Enfermedades de los Caballos , Tráquea , Animales , Caballos/microbiología , Asma/microbiología , Tráquea/microbiología , Estudios de Casos y Controles , Enfermedades de los Caballos/microbiología , Hongos/aislamiento & purificación , Estudios Retrospectivos , Masculino , Femenino , Líquido del Lavado Bronquioalveolar/microbiologíaRESUMEN
BACKGROUND: Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health. RESULTS: Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease. CONCLUSIONS: Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe's occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops. Video Abstract.
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Bacterias , Hongos , Metaboloma , Microbiota , Enfermedades de las Plantas , Rizoma , Zingiber officinale , Zingiber officinale/microbiología , Rizoma/microbiología , Enfermedades de las Plantas/microbiología , Bacterias/clasificación , Bacterias/metabolismo , Bacterias/genética , Bacterias/aislamiento & purificación , Hongos/clasificación , Hongos/genética , Hongos/metabolismo , Hongos/aislamiento & purificación , Microbiología del Suelo , BiodiversidadRESUMEN
Objective: To ascertain the prevalence of asthma attacks among archivists and identify the associated occupational factors in this understudied professional population. Methods: We conducted a cross-sectional, questionnaire-based study among 1,002 archival workers. A multiple logistic regression was conducted to identify the association between asthma attacks and occupational exposures. The Strobe Protocol was applied. Results: 999 workers were included in the final analysis with the asthma prevalence of 33.3%. Main factors associated with asthma attacks (OR [95% CI]) were the presence of chemically irritating odors (2.152 [1.532-3.024]), mold odors (1.747 [1.148-2.658]), and insects (1.409[1.041-1.907]). A significant synergistic effect was observed between chemical irritants and mold, the odds ratio was 7.098 (95% CI, 4.752-10.603). Conclusion: There was a high prevalence of asthma attacks among archival workers, an under-studied population. Chemical irritants, molds and insects were associated with their asthma attacks. Notably, this study's data analysis has revealed a strong synergy (OR = 7.098) between chemical odors and molds in the workplace. While the existing international literature on this specific interaction remains somewhat limited, previous studies have already demonstrated the potential for chemical irritants, such as sulfur dioxide and ozone, to synergistically interact with inhalable allergens, including fungi, molds and dust mites. Consequently, this interaction seems to exacerbate asthma symptoms and perpetuate untreated exposure. Furthermore, in damp and damaged buildings, the presence of microbial components, such as cellular debris or spores released during fungal growth can trigger an inflammatory response, potentially served as a shared pathway for the development of asthma among individuals exposed to these hazardous factors.
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Asma , Hongos , Exposición Profesional , Humanos , Estudios Transversales , Masculino , Adulto , Femenino , Asma/epidemiología , Asma/etiología , Exposición Profesional/efectos adversos , Exposición Profesional/estadística & datos numéricos , Prevalencia , Encuestas y Cuestionarios , Persona de Mediana Edad , Hongos/aislamiento & purificación , Factores de Riesgo , Salud Pública , Odorantes , Irritantes/efectos adversosRESUMEN
Due to its nutritional value and health benefits, the date palm (Phoenix dactylifera L.) is an essential dietary food crop throughout Middle Eastern and African countries. Consumers are concerned about the possible microbial contamination of dates, especially since most dates arriving in local markets are unprocessed. The absence of processing increases the possibility of microbial contamination, which raises the probability of microbial contamination. This study aims to analyze and evaluate the variability of fungal and bacterial microbiota identified in the most popular date palm fruits in Saudi Arabia. The study assessed ten date variety fruits from the most popular date palm varieties for consumption in Saudi Arabia and analyzed the microbial count. Morphological and molecular characterization and comparison of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences identified 78 fungi, including 36 distinct species across 15 fungal genera. Alternaria, Fusarium, Curvilaria, Aspergillus, and Penicillium were the most frequent genera among the ten fruit cultivars studied, according to ITS-rDNA sequence analysis. Furthermore, 36 bacterial isolates were obtained from ten date varieties studied, each with a unique colony morphology. These isolates were identified based on sequence alignment and comparison of their 16S rDNA internal spacer regions to those available in public databases. The results showed that the bacterial isolates included 15 species from five bacterial genera. The results suggested that Bacillus, Stenotrophomonas, and Brucella were the prevailing genera among the ten tested fruit varieties. Some bacterial genera, such as Brucella, Achromobacter, and Stenotrophomonas, are well-known potential human pathogens. Chaetomium globosum was also recognized as air pollution causing adverse health effects such as allergies and as the causal agent of human fungal infections among the tested date varieties; the Rashodiah type exhibited the highest fungal contamination, whereas the Sagai variety displayed the lowest fungal contamination. Conversely, the Sukkari, Barhi, and Mejdool varieties were the most contaminated with bacteria among the ten tested varieties, while the Khalas variety showed the least bacterial contamination. To the best of the authors' knowledge, this study provides the initial comprehensive account of the molecular and morphological identification of all fungal and bacterial genera associated with date palm (P. dactylifera) fruits.
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Bacterias , Biodiversidad , Frutas , Hongos , Microbiota , Phoeniceae , Phoeniceae/microbiología , Phoeniceae/genética , Frutas/microbiología , Microbiota/genética , Hongos/clasificación , Hongos/genética , Hongos/aislamiento & purificación , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Arabia Saudita , Filogenia , ARN Ribosómico 16S/genética , ADN Espaciador Ribosómico/genéticaRESUMEN
Cystic fibrosis (CF) is a genetic disorder characterized by chronic microbial colonization and inflammation of the respiratory tract (RT), leading to pulmonary exacerbation (PEx) and lung damage. Although the lung bacterial microbiota has been extensively studied, the mycobiome remains understudied. However, its importance as a contributor to CF pathophysiology has been highlighted. The objective of this review is to provide an overview of the current state of knowledge regarding the mycobiome, as described through NGS-based studies, in patients with CF (pwCF).Several studies have demonstrated that the mycobiome in CF lungs is a dynamic entity, exhibiting a lower diversity and abundance than the bacterial microbiome. Nevertheless, the progression of lung damage is associated with a decrease in fungal and bacterial diversity. The core mycobiome of the RT in pwCFs is mainly composed of yeasts (Candida spp., Malassezia spp.) and molds with lower abundance. Some fungi (Aspergillus, Scedosporium/Pseudallescheria) have been demonstrated to play a role in PEx, while the involvement of others (Candida, Pneumocystis) remains uncertain. The "climax attack" ecological model has been proposed to explain the complexity and interplay of microbial populations in the RT, leading to PEx and lung damage. NGS-based studies also enable the detection of intra- and interkingdom correlations between fungi and bacteria. Further studies are required to ascertain the biological and pathophysiological relevance of these correlations. Finally, with the recent advent of CFTR modulators, our understanding of the pulmonary microbiome and mycobiome in pwCFs is about to change.
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Fibrosis Quística , Metagenómica , Micobioma , Fibrosis Quística/microbiología , Fibrosis Quística/complicaciones , Humanos , Metagenómica/métodos , Hongos/genética , Hongos/clasificación , Hongos/aislamiento & purificación , Sistema Respiratorio/microbiología , Bacterias/genética , Bacterias/clasificación , Bacterias/aislamiento & purificación , Pulmón/microbiología , MicrobiotaRESUMEN
A significant number of microorganisms inhabit the intestinal tract or the body surface of insects. While the majority of research on insect microbiome interaction has mainly focused on bacteria, of late multiple studies have been acknowledging the importance of fungi and have started reporting the fungal communities as well. In this study, high-throughput sequencing was used to compare the diversity of intestinal fungi in Delia antiqua (Diptera: Anthomyiidae) at different growth stages, and effect of differential fungi between adjacent life stages on the growth and development of D. antiqua was investigated. The results showed that there were significant differences in the α and ß diversity of gut fungal communities between two adjacent growth stages. Among the dominant fungi, genera Penicillium and Meyerozyma and family Cordycipitaceae had higher abundances. Cordycipitaceae was mainly enriched in the pupal and adult (male and female) stages, Penicillium was mainly enriched in the pupal, 2nd instar and 3rd instar larval stages, and Meyerozyma was enriched in the pupal stage. Only three fungal species were found to differ between two adjacent growth stages. These three fungal species including Fusarium oxysporum, Meyerozyma guilliermondii and Penicillium roqueforti generally inhibited the growth and development of D. antiqua, with only P. roqueforti promoting the growth and development of female insects. This study will provide theoretical support for the search for new pathogenic microorganisms for other fly pests control and the development of new biological control strategies for fly pests.
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Dípteros , Hongos , Microbioma Gastrointestinal , Larva , Animales , Dípteros/microbiología , Dípteros/crecimiento & desarrollo , Hongos/clasificación , Hongos/aislamiento & purificación , Hongos/genética , Larva/microbiología , Larva/crecimiento & desarrollo , Masculino , Femenino , Pupa/microbiología , Pupa/crecimiento & desarrollo , Biodiversidad , Estadios del Ciclo de Vida , MicobiomaRESUMEN
BACKGROUND: Cutaneous infectious granulomas (CIG) are localized and chronic skin infection caused by a variety of pathogens such as protozoans, bacteria, worms, viruses and fungi. The diagnosis of CIG is difficult because microbiological examination shows low sensitivity and the histomorphological findings of CIG caused by different pathogens are commonly difficult to be distinguished. OBJECTIVE: The objective of this study is to explore the application of mNGS in tissue sample testing for CIG cases, and to compare mNGS with traditional microbiological methods by evaluating sensitivity and specificity. METHODS: We conducted a retrospective study at the Department of Dermatology of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from January 1st, 2020, to May 31st, 2024. Specimens from CIG patients with a clinical presentation of cutaneous infection that was supported by histological examination were retrospectively enrolled. Specimens were delivered to be tested for microbiological examinations and mNGS. RESULTS: Our data show that mNGS detected Non-tuberculosis mycobacteria, Mycobacterium tuberculosis, fungi and bacteria in CIG. Compared to culture, mNGS showed a higher positive rate (80.77% vs. 57.7%) with high sensitivity rate (100%) and negative predictive value (100%). In addition, mNGS can detect more pathogens in one sample and can be used to detect variable samples including the samples of paraffin-embedded tissue with shorter detective time. Of the 21 patients who showed clinical improvement within a 30-day follow-up, eighteen had their treatments adjusted, including fifteen who continued treatment based on the results of mNGS. CONCLUSIONS: mNGS could provide a potentially rapid and effective alternative detection method for diagnosis of cutaneous infectious granulomas and mNGS results may affect the clinical prognosis resulting from enabling the patients to initiate timely treatment.
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Granuloma , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Estudios Retrospectivos , Masculino , Femenino , Persona de Mediana Edad , Adulto , Granuloma/microbiología , Granuloma/diagnóstico , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Bacterias/aislamiento & purificación , Bacterias/genética , Bacterias/clasificación , Anciano , Sensibilidad y Especificidad , Hongos/aislamiento & purificación , Hongos/genética , Hongos/clasificación , Adulto Joven , Metagenómica/métodos , Enfermedades Cutáneas Infecciosas/diagnóstico , Enfermedades Cutáneas Infecciosas/microbiología , Adolescente , Piel/microbiología , Piel/patología , NiñoRESUMEN
Pinellia ternata (Thunb.) Breit is an important traditional Chinese medicine. In North China, conventional flat planting of P. ternate is prone to root rot during the rainy season, leading to severe yield loss. Variations in planting patterns (e.g., ridge planting) can effectively alleviate this situation. However, the relationship between planting patterns and the changes induced by rhizosphere microbiome still needs to be determined. In this study, we clarified the effect of ridge planting on the yield of P. ternata and rhizosphere microbial community using high-throughput amplicon sequencing of 16S rRNA. Field experiments showed that ridge planting could increase the yield of P. ternata by 72.69% compared with flat planting. The high-throughput sequencing results demonstrated that fungal and bacterial communities in rhizosphere siols of flat and ridge planting showed obvious difference in diversity, structure, relative abundance, and community composition. The fungal phyla Zygomycota, Basidiomycota, Glomeromycota, and the bacterial phyla Chlamydiae, Tenericutes, and Hydrogenedentes were present in a higher relative abundance in the rhizosphere of ridge planting. Adonis multivariate analysis of variance results showed that 29 bacterial genera were significantly up/down-regulated, and only 4 fungal genera were changed considerably in ridge planting soil, indicating that the bacterial community composition varied significantly between the two treatments. Correlation analysis revealed that the yield of P. ternata was positively correlated with fungal genera Emericellopsis while negatively correlated with bacterial genera Acetobacter, Iamia, and fungal genera Thielavia. Overall, this study showed that ridge cropping significantly impacts the diversity and composition of the rhizosphere microbiome. It creates an environment favorable for crop growth and can be an effective planting strategy for P. ternata in areas with irrigation and high monsoon rainfall in North China.
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Microbiota , Pinellia , Rizosfera , Microbiología del Suelo , China , Pinellia/microbiología , ARN Ribosómico 16S/genética , Bacterias/genética , Bacterias/clasificación , Bacterias/aislamiento & purificación , Hongos/genética , Hongos/clasificación , Hongos/aislamiento & purificación , Raíces de Plantas/microbiología , Raíces de Plantas/crecimiento & desarrollo , Secuenciación de Nucleótidos de Alto RendimientoRESUMEN
BACKGROUND: The commercialization of space travel will soon lead to many more people living and working in unique built environments similar to the International Space Station, which is a specialized closed environment that contains its own indoor microbiome. Unintended microbial growth can occur in these environments as in buildings on Earth from elevated moisture, such as from a temporary ventilation system failure. This growth can drive negative health outcomes and degrade building materials. We need a predictive approach for modeling microbial growth in these critical indoor spaces. RESULTS: Here, we demonstrate that even short exposures to varying elevated relative humidity can facilitate rapid microbial growth and microbial community composition changes in dust from spacecraft. We modeled fungal growth in dust from the International Space Station using the time-of-wetness framework with activation and deactivation limited growth occurring at 85% and 100% relative humidity, respectively. Fungal concentrations ranged from an average of 4.4 × 106 spore equivalents per milligram of dust in original dust with no exposure to relative humidity to up to 2.1 × 1010 when exposed to 100% relative humidity for 2 weeks. As relative humidity and time-elevated increased, fungal diversity was significantly reduced for both alpha (Q < 0.05) and beta (R2 = 0.307, P = 0.001) diversity metrics. Bacteria were unable to be modeled using the time-of-wetness framework. However, bacterial communities did change based on constant relative humidity incubations for both beta (R2 = 0.22, P = 0.001) and alpha diversity decreasing with increasing moisture starting at 85% relative humidity (Q < 0.05). CONCLUSION: Our results demonstrate that moisture conditions can be used to develop and predict changes in fungal growth and composition onboard human-occupied spacecraft. This predictive model can be expanded upon to include other spacecraft environmental factors such as microgravity, elevated carbon dioxide conditions, and radiation exposure. Understanding microbial growth in spacecraft can help better protect astronaut health, fortify spacecraft integrity, and promote planetary protection as human activity increases in low-Earth orbit, the moon, Mars, and beyond. Video Abstract.
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Polvo , Hongos , Humedad , Microbiota , Vuelo Espacial , Nave Espacial , Polvo/análisis , Hongos/clasificación , Hongos/aislamiento & purificación , Bacterias/clasificación , Bacterias/aislamiento & purificación , Humanos , Microbiología del AireRESUMEN
Species interactions between bats and fungi are poorly known. We documented the association between fungal and bat diversities along a landscape gradient. Ten, eight, and seven bat species were captured in conserved, semi-conserved, and urban sites, respectively. Eptesicus fuscus, Myotis ciliolabrum and Corynorhinus townsendii were the most abundant in conserved and semi-conserved sites. E. fuscus, Myotis velifer, and Lasiurus cinereus were abundant in urban sites. C. townsendii was the least abundant bat. A total of 15 cultivated fungi genera included the fungal diversity in bats, of which nine fungi genera were shared along the landscape gradient. Penicillium and Aspergillus were the most abundant genera, and Aureobasidium, Bispora, Stachybotrys, and Verticillium were only documented in the conserved sites. We observed a higher fungal diversity associated with bat species along this landscape gradient. The individual site-based accumulation curves of fungal diversity showed significant decreasing values along the conserved, semi-conserved, and urban sites, respectively. In conserved and urban sites, M. californicus and M. velifer showed the highest fungal diversity, respectively. E. fuscus was associated to the fungi genera Scopulariopsis, Alternaria, Penicillium and Beauveria; L. cinereus to Cladosporium and Aspergillus, and M. velifer to Alternaria sp1, Bispora and Trichoderma. Conserved sites showed both high bat and fungal diversities [species richness and abundance] compared to semi-conserved and urban sites. More studies associating bat and fungal diversities in other ecosystems are needed to corroborate this pattern.
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Biodiversidad , Quirópteros , Hongos , Quirópteros/microbiología , México , Animales , Hongos/clasificación , Hongos/aislamiento & purificación , Hongos/genética , EcosistemaRESUMEN
The North American (NA) porcupine (Erethizon dorsatum) is a rodent species with specialized hair structures called quills designed to detach and penetrate into tissues of any human or animal coming into contact with them. The objective of this study was to characterize the fungal flora of the quills in the region of the rosette in wild NA porcupines to further define health risks to NA porcupines and any animal coming into contact with the quills. A total of 17 adult NA porcupines were sampled, and fungal culture was performed. Fungal organisms were cultured from 15 (88.2%) of 17 samples. Thirty-three isolates of 10 different fungal genera were cultured. The most frequently isolated fungi were Lodderomyces elongisporus (n = 7, 41.2%), Candida spp. (n = 3, 17.6%), and Penicillium spp. (n = 2, 11.8%). Eleven (64.7%) individuals grew multiple fungal organisms. In humans and animals quilled by porcupines, fungal culture should be considered in cases of infection, and if isolates resembling Candida spp. are isolated, matrix-assisted laser desorption-ionization time of flight or molecular methods are necessary to rule out L. elongisporus.
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Puercoespines , Puercoespines/microbiología , Animales , Hongos/aislamiento & purificación , Hongos/clasificación , Femenino , Masculino , Cabello/microbiologíaRESUMEN
Mycetoma can be caused either by fungi or aerobic Actinomycetes. A precise identification of the causal agents is critical for the therapeutic outcome. Thus, this study aimed to identify the pathogens of mycetoma using 16S/ITS rRNA gene polymerase chain reaction (PCR) followed by Sanger sequencing directly on grains. In sum, 32 samples including 15 black grains, 12 red grains, and five white/yellow grains collected from patients with mycetoma at the Aristide Le Dantec University Hospital in Dakar, Senegal, between October 2014 and September 2020 were submitted to PCR/sequencing. For black grain eumycetoma, the ITS rRNA region was targeted. Similarly, the 16S rRNA gene was targeted for red grain actinomycetoma. These two regions were targeted in parallel for white/yellow grains, which could be of either bacterial or fungal origin. The age of the patients ranged from 14 to 72 years with a mean age of 36 ± 14 years. Thirteen (86%) of the 15 samples with black grains, were successfully sequenced with only one established eumycetoma pathogen, Madurella mycetomatis identified in 11 (73%). Cladosporium sphaerospermum was identified in one sample. For the 16S rRNA sequencing of red grains, a 58.3% (7/12) success rate was obtained with Actinomadura pelletieri identified in six samples. Among the five samples sequenced twice, the 16S rRNA allowed us to identify the causative agent in 2 cases, A. madurae in one, and A. geliboluensis in the other. The ITS rRNA identified 3 fungi, of which none was a mycetoma agent. Overall, direct 16S/ITS rRNA sequencing of the grains for detecting and identifying mycetoma pathogens was successful in 59.4% of cases. Fungi, led by M. mycetomatis, were the predominant pathogens identified. Two probable new mycetoma agents, C. sphaerospermum, and A. geliboluensis were identified and both deserve to be confirmed in further studies.
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Hospitales Universitarios , Micetoma , Reacción en Cadena de la Polimerasa , ARN Ribosómico 16S , Micetoma/microbiología , Micetoma/diagnóstico , Humanos , ARN Ribosómico 16S/genética , Adulto , Senegal , Persona de Mediana Edad , Masculino , Adolescente , Adulto Joven , Anciano , Femenino , Reacción en Cadena de la Polimerasa/métodos , Proyectos Piloto , Análisis de Secuencia de ADN , ADN Espaciador Ribosómico/genética , Madurella/genética , Madurella/aislamiento & purificación , Hongos/genética , Hongos/aislamiento & purificación , Hongos/clasificación , ADN de Hongos/genética , Actinobacteria/genética , Actinobacteria/aislamiento & purificación , Actinobacteria/clasificaciónRESUMEN
Background: Metagenomic next-generation sequencing (mNGS), which provides untargeted and unbiased pathogens detection, has been extensively applied to improve diagnosis of pulmonary infection. This study aimed to compare the clinical performance between mNGS and targeted NGS (tNGS) for microbial detection and identification in bronchoalveolar lavage fluid (BALF) from kidney transplantation recipients (KTRs). Methods: BALF samples with microbiological results from mNGS and conventional microbiological test (CMT) were included. For tNGS, samples were extracted, amplified by polymerase chain reaction with pathogen-specific primers, and sequenced on an Illumina Nextseq. Results: A total of 99 BALF from 99 KTRs, among which 93 were diagnosed as pulmonary infection, were analyzed. Compared with CMT, both mNGS and tNGS showed higher positive rate and sensitivity (p<0.001) for overall, bacterial and fungal detection. Although the positive rate for mNGS and tNGS was comparable, mNGS significantly outperformed tNGS in sensitivity (100% vs. 93.55%, p<0.05), particularly for bacteria and virus (p<0.001). Moreover, the true positive rate for detected microbes of mNGS was superior over that of tNGS (73.97% vs. 63.15%, p<0.05), and the difference was also significant when specific for bacteria (94.59% vs. 64.81%, p<0.001) and fungi (93.85% vs. 72.58%, p<0.01). Additionally, we found that, unlike most microbes such as SARS-CoV-2, Aspergillus, and EBV, which were predominantly detected from recipients who underwent surgery over 3 years, Torque teno virus (TTV) were principally detected from recipients within 1-year post-transplant, and as post-transplantation time increased, the percentage of TTV positivity declined. Conclusion: Although tNGS was inferior to mNGS owing to lower sensitivity and true positive rate in identifying respiratory pathogens among KTRs, both considerably outperformed CMT.